Taphonomy is the study of processes and patterns of fossil preservation. The exquisite fossils of the Rochester Shale have inspired a number of studies of taphonomy or fossil preservation (see Taylor and Brett, 1997). Distinctive modes of preservation typify different groups of fossils. Calcitic fossils, such as brachiopods, bryozoans, echinoderms and corals tend to preserve very well, with much detail except in areas where the Rochester Shale has undergone late stage dolomitization; there, the fossils tend to be "ghosted" (shells partially dissolved) and their detail obscured. Originally aragonitic fossils, such as some bivalves, tend to be poorly preserved, highly flattened molds. Most beds also show strong compaction of fossils, which has deformed them to varying extents.

Biostratinomy includes the study of processes that are imposed upon organic remains essentially from the death of organisms to their final burial; these include mortality itself and necrotic (decay) processes. Sources of organic remains include both normal and mass mortality as well as the shedding of parts during the lifetimes of some types of animals, such as molt parts of trilobites. Rarely, skeletons are buried precisely in life position and there are examples of probable live burial in the Rochester Shale, including complete cystoids that are simply toppled where they stood. More commonly, skeletal remains may be reoriented. Bodies or skeletons may become preferentially oriented by currents or waves or even by bioturbation (burrowing and other disturbance by organisms) prior to burial. The dish-shaped valves of brachiopods are most stable in convex up orientations and are commonly preserved in convex upward pavements of Striispirifer valves (Figures xxvii - xxix and 93). Rarely, when valves are suspended by storm waves and allowed to settle from water they will flip and land convex downward. The occurrence of edrioasteroids on the undersides of convex downward shells from the Rochester Shale implies such a mode of emplacement; the shells were lifted off the seafloor at the final moment and then re-settled burying the edrioasteroids on the bottom side (Brett, 1983).

Fossils with a long axis commonly show a slightly to strongly preferred alignment. This may affect conical shells such as cephalopod, which tend to rotate such that their long axis parallels the current direction with the apex pointing upstream. Multiple specimens of Dalmanites trilobites on some bedding planes appear to show a high degree of parallel alignment (Figures xxvi and 395). These patterns may reflect slight current orientation of dead carcasses in the aftermath of storms during which gradient currents flowed basinward following storm surges.

Soft tissues degrade very rapidly upon death even in anoxic settings; connective tissues are somewhat more resistant than most soft parts but still tend to breakdown in days to months, releasing articulated skeletal parts. Brachiopods had various potentials for disarticulation. In spiriferids like Striispirifer the pedicle and brachial valves would have become readily separated after death. In contrast, the interlocking hinge teeth of rhynchonellid and some atrypid brachiopods (Figures 98 and 99; 69 and 70) would have maintained valve articulation for prolonged periods. The hinge teeth would have to have been physically broken to allow these brachiopods to disarticulate, and consequently they are commonly intact even in beds in which all other brachiopods occur as separated valves. Thus, different species show distinct differences in preservation. For example, in bulk samples from the Homocrinus beds at Lockport, Brett (1978a) found that all specimens of Atrypa reticularis and Stegerhynchus were articulated, whereas of 343 specimens of Striispirifer niagarensis, 85 were articulated but 258 occurred as separated valves.

Following disarticulation, skeletal parts may become fragmented and abraded, especially in high-energy settings or chemically corroded, mainly in deeper water settings. Many of the densely packed shell-bryozoan beds show evidence of substantial disarticulation of brachiopods and some fragmentation of valves and most bryozoans.This probably represents prolonged periods of normal mortality and residence of skeletal remains on the seafloor. These are time-averaged deposits representing mixtures of the remains of multiple generations of organisms that occupied the seafloor and accumulated.